PCA

## PC_ 1 
## Positive:  Hmgb2, Lgals1, S100a6, S100a4, Stmn1, Pclaf, Hist1h2ap, Hist1h1b, Hist1h2ae, Mki67 
## Negative:  Rps24, Malat1, Rps27, Rps29, Tpt1, Rplp1, Rps15a, Rpl12, Rpl23, Ccl5 
## PC_ 2 
## Positive:  S100a6, S100a4, Lgals1, S100a10, Tmsb4x, Lgals3, Crip1, Gzmb, Gzma, Ccl5 
## Negative:  Top2a, Hist1h2ae, Hist1h3c, Hist1h2ab, Hist1h2ap, Hist1h4d, Nusap1, Hist2h2ac, Mki67, Hist1h1b 
## PC_ 3 
## Positive:  Ccl5, Malat1, Klrk1, Ikzf2, Fcer1g, Klra7, Cenpf, Klre1, Ube2c, Nusap1 
## Negative:  Dapl1, Dut, Rplp1, Ptma, Rps8, Lgals3, 1500009L16Rik, Rps20, Rrm2, Hsp90ab1 
## PC_ 4 
## Positive:  Dapl1, Ifi27l2a, Malat1, Ube2c, Cenpa, Cenpf, Ccr9, Fos, Igfbp4, Cd8b1 
## Negative:  Ccl5, Ctla2a, Ly6c2, Klre1, Hist1h2ae, Klra7, Rrm2, Dut, Hist1h1b, Hist1h2ap
## [1] "Contribution des gènes pour les PC"

## [1] "Heatmaps avec les 20 gènes contribuants le plus dans la PC"

Choose 11 CP for the continuation

UMAP

DE befor clusterization

## [1] "VV-B8R"         "Ly49p-CD8ab"    "VV-Ly49p-CD8aa" "Ly49p-CD8aa"   
## [5] "VV-Ly49p-CD8ab" "Naive"          "Ly49n"
## # A tibble: 14 × 7
## # Groups:   cluster [7]
##        p_val avg_log2FC pct.1 pct.2 p_val_adj cluster        gene     
##        <dbl>      <dbl> <dbl> <dbl>     <dbl> <fct>          <chr>    
##  1 0              4.30  0.961 0.251 0         VV-B8R         S100a4   
##  2 0              4.13  0.743 0.217 0         VV-B8R         Hist1h2ap
##  3 3.60e-217      1.03  0.934 0.633 5.53e-213 Ly49p-CD8ab    Fos      
##  4 4.13e-174      0.878 0.878 0.576 6.34e-170 Ly49p-CD8ab    Dusp2    
##  5 0              1.23  0.835 0.282 0         VV-Ly49p-CD8aa Ikzf2    
##  6 5.22e-174      1.03  0.725 0.388 8.01e-170 VV-Ly49p-CD8aa Klra7    
##  7 8.81e-229      1.21  0.854 0.327 1.35e-224 Ly49p-CD8aa    Ikzf2    
##  8 6.08e-175      1.20  0.948 0.65  9.32e-171 Ly49p-CD8aa    Fos      
##  9 1.28e-180      0.589 0.806 0.485 1.97e-176 VV-Ly49p-CD8ab Ms4a4c   
## 10 2.06e-174     -1.06  0.249 0.551 3.16e-170 VV-Ly49p-CD8ab Itga4    
## 11 8.51e-236      1.55  0.574 0.171 1.31e-231 Naive          Dapl1    
## 12 5.71e-242      1.02  0.904 0.65  8.75e-238 Naive          Lef1     
## 13 9.33e- 12      0.533 0.65  0.386 1.43e-  7 Ly49n          Tnfaip3  
## 14 3.44e- 10     -0.825 0.153 0.407 5.28e-  6 Ly49n          Klre1

Clustree and clusterization

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 1.0000
## Number of communities: 1
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9500
## Number of communities: 5
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.9231
## Number of communities: 7
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8995
## Number of communities: 9
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8820
## Number of communities: 9
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8672
## Number of communities: 11
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8538
## Number of communities: 12
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8421
## Number of communities: 13
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8305
## Number of communities: 13
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8193
## Number of communities: 14
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8095
## Number of communities: 14
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7998
## Number of communities: 15
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7912
## Number of communities: 16
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7840
## Number of communities: 18
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7787
## Number of communities: 18
## Elapsed time: 0 seconds
## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.7715
## Number of communities: 20
## Elapsed time: 0 seconds

## Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck
## 
## Number of nodes: 8310
## Number of edges: 266478
## 
## Running Louvain algorithm...
## Maximum modularity in 10 random starts: 0.8672
## Number of communities: 11
## Elapsed time: 0 seconds

DE after clusterization

##  [1] "0"  "1"  "2"  "3"  "4"  "5"  "6"  "7"  "8"  "9"  "10"
## # A tibble: 21 × 7
## # Groups:   cluster [11]
##        p_val avg_log2FC pct.1 pct.2 p_val_adj cluster gene  
##        <dbl>      <dbl> <dbl> <dbl>     <dbl> <fct>   <chr> 
##  1 0              1.42  0.966 0.601 0         0       Fos   
##  2 0              1.22  0.949 0.624 0         0       Fosb  
##  3 4.57e-180      1.04  0.734 0.388 7.01e-176 1       Klra7 
##  4 7.20e-140      0.907 0.628 0.312 1.10e-135 1       Klrk1 
##  5 1.90e- 98     -1.14  0.219 0.502 2.92e- 94 2       Itga4 
##  6 3.96e-278      1.66  0.595 0.165 6.08e-274 3       Dapl1 
##  7 1.43e-249      1.03  0.903 0.649 2.19e-245 3       Lef1  
##  8 6.99e-104      0.816 0.56  0.258 1.07e- 99 4       Gzmm  
##  9 8.63e- 81      0.527 0.848 0.547 1.32e- 76 4       Ms4a4c
## 10 1.32e-218      2.95  0.906 0.297 2.02e-214 5       S100a4
## # … with 11 more rows